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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctgattcgtgatgcgtgtgcatatttgattgatagtttgtttccttgtttgggtgaagaggttttggtgattgatttggtcttgtttttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTATGCCTGCAGGAACTGTGACCACCAG

Basic information

species Oryza sativa
transcript LOC_Os12g37370.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g37370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ22675 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------------------------------------------gtgagctgattcgtgatgcgtgtgcatatttgattgatagtttgtttccttgtttgggtgaagaggttttggtgattgatttg----gtcttg--tttttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTATGCCTGCAGGAACTGTGACCACCAG
| | || | || | | | | || || | || | ||| | | ||||| | | | ||| | ||| | | |||| |||||||| ||||||||||||||||| |||| || ||||| |||| |||||||| ||||||| ||||||||
gtgagttgggtttgctcgtctcgcgtcgctggagctcgcgctcggcggcatcttgagtaactccgcattgggtgtcaggaaattcattgatttcctcgaacgaatgaatgctcgtcgcattgaaagtgtggtttttgctcgtggcattgaaaggctttggatcccctcttgcagTAACAACATCCTGTATCCCAAGGAGGACCGGGATCAAAAGATCTTGCTGTATGCCTGTCGGAACTGCGACCACCAA

upper sequence: LOC_Os12g37370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ11827 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------------------------------------------gtgagctgattcgtgatgcgtgtgcatatttgattgatagtttgtttccttgtttgggtgaagaggttttggtgattgatttg----gtcttg--tttttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTATGCCTGCAGGAACTGTGACCACCAG
| | || | || | | | | || || | || | ||| | | ||||| | | | ||| | ||| | | |||| |||||||| ||||||||||||||||| |||| || ||||| |||| |||||||| ||||||| ||||||||
gtgagttgggtttgctcgtctcgcgtcgctggagctcgcgctcggcggcatcttgtgtaactccgcattgggtgtcgggaaattcattgattttctcgaacgaatgaatgctcgtcgcattgaaagtgtggtttttgctcgtggcattgaaaggctttggatcccctcttgcagTAACAACATCCTGTATCCCAAGGAGGACCGGGATCAAAAGATCTTGCTGTATGCCTGTCGGAACTGCGACCACCAA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|33817971|gb|CF334813.1|CF334813
EST:     TCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGCCGCGAATG                         CAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
genomic: TCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGCCGCGAATGgtgagctgat ... ttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
EST: gi|112787231|gb|EE592303.1|EE592303
EST:     TCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGGCGCGAATG                         CAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
genomic: TCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGCCGCGAATGgtgagctgat ... ttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
EST: gi|88584285|gb|CI701828.1|CI701828
EST:     TCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGCCGCGAATG                         CAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
genomic: TCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGCCGCGAATGgtgagctgat ... ttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
EST: gi|33814350|gb|CF333047.1|CF333047
EST:     TCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGCCGCGAATG                         CAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
genomic: TCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGCCGCGAATGgtgagctgat ... ttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
EST: gi|86906467|gb|CI294590.1|CI294590
EST:     TTTGCCGCGAATG                         CAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
genomic: TTTGCCGCGAATGgtgagctgat ... ttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
EST: gi|58591666|gb|CF989974.1|CF989974
EST:     TCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGCCGCGAATG                         CAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA
genomic: TCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGCCGCGAATGgtgagctgat ... ttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 66 (upstream exon), 68 (downstream exon)
Score: 6

GAATATAAAGATCTGAAAGAGGCAAGCAGACAAGGTCAGGTCAGGTCAGGTCAGAGGAGAAGCTAGCAGCCATGAGTACCATGAAATTTTGCCGCGAATGgtgagctgat ... ttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTATGCCTGCAGGAACTGTGACCACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgtttgggtgaagaggttttggtgattgatttggtcttgtttttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTATGCCTGCAGGAACTGTGACCACCAG
                          gattgat  putative branch site (score: 6)
 tcttgttttt  putative PPT
 attgattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctgattcgtgatgcgtgtgcatatttgattgatagtttgtttccttgtttgggtgaagaggttttggtgattgatttggtcttgtttttgttggcagCAACAACATACTGTATCCCAAGGAGGATAGGGACCAGAAGATTCTGCTCTATGCCTGCAGGAACTGTGACCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG